Dr. Robert Clarke's Publications

(See also Publications from Leena Hilakivi-Clarke's Laboratory)
 

Year 2019
  1. Clarke, R. “Introduction: The unfolded protein response.” In: The Unfolded Protein Response in Cancer: Ed: Clarke, R. Springer Nature, pp1-15, 2019.
  2. Sengupta, S., Jordan, V.C. & Clarke, R. “Role of protein translation in unfolded protein response.” In: The Unfolded Protein Response in Cancer: Ed: Clarke, R. Springer Nature, pp109-120, 2019.
  3. Hu, R & Clarke, R. “Roles of spliced and unspliced XBP1 in breast cancer.” In: The Unfolded Protein Response in Cancer: Ed: Clarke, R. Springer Nature, pp121-132, 2019.
  4. Sengupta, S. Sevigny, C., Jordan, V.C. & Clarke, R. “Estrogen induced apoptosis in breast cancers is phenocopied by blocking de-phosphorylation of eIF23-alpha protein.” Mol Cancer Res, 17: 918-928, 2019.
  5. Clarke, R., Tyson, J.J., Tan, M., Baumann, W., Xuan, J & Wang, Y. “Systems biology: quantitative multiscale modeling in research in breast and other cancers.” Endocr Relat Cancer, in press, doi: 10.1530/ERC-18-0309, 2019.
  6. Pulliam, N., Tang, J. Wang, W., Fang, F., Sood, R. O’Hagan, H.M., Miller, K.D., Clarke, R. & Nephew, K. “Poly-ADP-ribosylation of Estrogen Receptor-alpha by PARP1 Mediates Antiestrogen Resistance in Human Breast Cancer Cells.” Cancers, doi: 10.3390/cancers11010043, 2019.
  7. Yu, W., Zhang, X., Carney, E., Hu, R., Andrade, F., Clarke, R., FitzGerald, K, & Hilakivi-Clarke, L.A. “Effects of jaeumkanghwa-tang on tamoxifen responsiveness in a preclinical ER+ breast cancer model.” Endocr Relat Cancer 26: 339-353, 2019.
  8. Shajahan-Haq, A.N., Demas, D.M., Demo, S., Fallah, Y., Clarke, R., Nephew, K.P., Althouse, S., Sandusky, G. & He, W. “Glutamine metabolism drives growth in advanced hormone receptor positive breast cancer.” Front Oncol, in press, 2019
  9. Clarke, R. “The unfolded protein response as an integrator of response to endocrine therapy in estrogen receptor positive breast cancer.” In: The Unfolded Protein Response in Cancer: Ed: Clarke, R. Springer Nature, pp163-180, 2019.
  10. Zhang, Y.-W., Nasto, R.E., Jablonski, S.A, Serebriiski, I.G., Surana, R., Murray, J., Johnson, M., Riggins, R.B., Clarke, R., Golemis, E.A. & Weiner, L.M. “RNA interference screening methods to identify proliferation determinants and mechanisms of resistance to immune attack.” Methods Enzymol, in press (doi.org/10.1016/bs.mie.2019.06.002) 2019.

Year 2018
  1. Wärri, A., Cook, K.L., Hu, R., Jin, L., Zwart, A., Soto-Pantoja, D.R., Liu, J., Finkel, T. & Clarke, R. “Autophagy and Unfolded Protein Response (UPR) signaling regulate progression of mammary gland involution by restraining apoptosis-driven irreversible changes.” Cell Death Discovery, 4:40 doi: 10.1038/s41420-018-0105-y, 2018 (13 pages as published online).
  2. Xu, S., Wang, X., Hilakivi-Clarke, L.A., Clarke, R. & Xuan, J. “Sparselo: a novel Bayesian approach to identify alternatively spliced isoforms from RNAseq data.” Bioinformatics, 34: 56-63, 2018.
  3. Chen, X., Gu, J., Wang, X., Jung, J.-G., Wang, T.-L., Hilakivi-Clarke, L.A., Clarke, R. & Xuan, J. “CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and RBA-seq data.” Bioinformatics, 34: 1733-1740, 2018.
  4. Kikkeri, K., Soltanian-Zadeh, S., Shajahan-Haq, A.N., Strobl, J. Clarke, R. & Agah, M. “Dielectrophoretic properties distinguish responses to estrogen and Fulvestrant in breast cancer cells.” Sens Actuators B Chem, 277: 186-194, 2018.

Year 2017
  1. Wang, X., Gu, J., Hilakivi-Clarke, L.A., Clarke, R. & Xuan, J. “DM-BLD: Differential methylation detection using a hierarchical Bayesian model exploiting local dependency.” Bioinformatics, 33(2):161-168, 2017.
  2. Chen, X., Shi, X., Hilakivi-Clarke, L., Shajahan-Haq, A.N., Clarke, R., Wang, Y. & Xuan, J. “PSSV: A novel pattern-based probabilistic approach for somatic structure variation identification.” Bioinformatics, 33:177-183, 2017.
  3. Zhang, Y.-W., Nasto, R., Jablonski, S.A., Serebriiski, I.G., Surana, R., Murray, J., Johnson, M., Riggins, R.B., Clarke, R., Golemis, E.A. & Weiner, L.M. “RNA interference to identify proliferation determinants in breast cancer cells.” Bio-Protocol, e2435. doi: 10.21769/BioProtoc.2435, 2017.
  4. Hilakivi-Clarke, L.A., Wärri, A., Bouker, K.B., Zhang, X., Cook, K.L., Jin, L., Zwart, A., Nguyen, N., Hu, R., Cruz, I.M., de Assis, S., Wang, X., Xuan, J., Wang, Y., Wehrenberg, B. & Clarke R. “In utero exposure to ethinyl estradiol predisposes to tamoxifen resistance and breast cancer recurrence in a preclinical model.” J Natl Cancer Inst, doi: 10.1093/jnci/djw188, 2017.
  5. Shajahan-Haq, A., Boca, S., Jin, L., Bhuvaneshwar, K., Gusev, Y., Cheema, A.K., Demas, D., Raghavan, K., Michalek, R., Madhavan, S. & Clarke, R. “EGR1 regulates cellular metabolism and survival in endocrine resistant breast cancer cells.” Oncotarget, 8: 96865-96884, 2017.
  6. Zhang, X., Cook, K.L., Wärri, A., Rosim, M., Riskin, J., Helferich, W., Doerge, D., Clarke, R. & Hilakivi-Clarke, L.A. “Lifetime genistein intake increases the response of mammary tumors to antiestrogen treatment and alters immune markers in rat mammary tumors.” Clin Cancer Res, 23:814-824, 2017.
  7. Shi, X., Banerjee, S., Chen, L., Hilakivi-Clarke, L., Clarke, R. & Xuan, J. “CyNetSVM: A cytoscape application for cancer biomarker identification using network constrained support vector machines.” PLoS ONE, 12:e0170482. doi: 10.1371/journal.pone.0170482, 2017.
  8. Soltanian-Zadeh, S., Kikkeri, K., Shajahan-Haq, A.N., Strobl, J., Clarke, R. & Agah, M. “Breast cancer cell Obatoclax response characterization using passive-electrode insulator-based dielectrophopresis.” Electrophoresis, 38: 1988-1995, 2017.
  9. Clarke, R. “Introduction: Cancer gene networks.” In: Cancer Gene Networks: Eds: Kasid, U. Clarke, R. Springer Nature, pp1-9, 2017.

Year 2016
  1. Zhang, Y.W., Nasto, R.E., Varghese, R., Jablonski, S.A., Serebriiskii, I.G., Surana, R., Bebu, I., Murray, J., Jin, L., Johnson, M., Riggins, R., Ressom., H., Petrocoin III, E., Clarke, R., Golemis, E.A. & Weiner, L.M. “Acquisition of estrogen independence induces TOB-1 mechanisms supporting breast cancer cell proliferation.” Oncogene, 35: 1643-1656, 2016.
  2. Cook, K.L., Soto-Pantoja, D.R., Clarke, P.A.G., Cruz, I., Zwart, A., Wärri, A., Roberts, D.D., & Clarke, R. “Endoplasmic reticulum stress protein, GRP78, modulates lipid metabolism to control breast tumor drug sensitivity and activate anti-tumor immunity.” Cancer Res, 76:5657-5670, 2016.
  3. Chen, X., Jung, J.-G., Shajahan-Haq, A., Clarke, R., Shih, I.-E., Wang, Y., Luca, M., Wang, T.L. & Xuan, J. “ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles.” Nucl Acids Res, 44: e65 (doi: 10.1093/nar/gkv1491), 2016.
  4. Klionsky, D.J., Abdelmohsen, K., Abe, A., Abelovich, H., ...Clarke, R.,... Zorzano, A. & Zughaier, S. (this project was led by Dr. Klionsky and the paper has too many authors to list all here; authors are listed alphabetically by surname). “Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).” Autophagy, 12: 1-222, 2016.
  5. Wang N, Hoffman EP, Chen L, Chen L, Zhang Z, Liu C, Yu G, Herrington DM, Clarke R, Wang Y. Mathematical modelling of transcriptional heterogeneity identifies novel markers and subpopulations in complex tissues. Scientific Reports, 6:18909. doi: 10.1038/srep18909, 2016.
  6. Bhuvaneshwar, K., Belouali, A., Singh, V., Johnson, R.M., Song, L. Alaoui, S., Harris, M.A., Clarke, R., Weiner, L.M., Gusev, Y., Madhavan, S. “G-DOC Plus - an integrative bioinformatics platform for precision medicine.” BMC Bioinformatics, 17:193 (doi: 10.1186/s12859-016-1010-0), 2016.
  7. Fang, H.-B., Huang, H, Clarke, R. & Tan, M. “Predicting multi-drug inhibition interactions based on the apoptosis signaling network and single drug dose-response information.” J Comp Sys Biol, 2: 101, 2016 (9 pages as published online).
  8. Sumis, A., Cook, K.L., Andrade, F.O., Hu, R., Kidney, E., Zhang, X., Kim, D., Carney, E., Nguyen, N., Yu, W., Bouker, K.B., Cruz, I., Clarke, R. & Hilakivi-Clarke, L. “Social isolation induces autophagy in the mouse mammary gland: link to increased mammary cancer risk.” Endocr-Relat Cancer, 23: 839-856, 2016
  9. Youssef, I. Clarke, R., Shih, I.-M., Wang, Y. & Yu, G. “Biologically inspired survival analysis based on integrating gene expression as mediator with genomic variants.” Comp Biol Med, 77: 231-239, 2016.

Year 2015
  1. Schwartz-Roberts, J.L., Cook, K.L., Chen, C., Shajahan-Haq, A.N., Axelrod, M., Wärri, A., Riggins, R.B., Jin, L., Haddad, B.R., Kallakury, B.V., Baumann, W.T. & Clarke, R. “Interferon regulatory factor-1 signaling regulates the switch between autophagy and apoptosis to determine breast cancer cell fate.” Cancer Res, 75: 1046-1055, 2015.
  2. Hu, R., Wärri, A., Jin, L., Zwart, A., Riggins, R.B. & Clarke, R. “NFκB signaling is required for XBP1 (U and S) mediated effects on antiestrogen responsiveness and cell fate decisions in breast cancer cells.” Mol Cell Biol, 35: 379-390, 2015.
  3. Shajahan-Haq, A.N., Cheema, M.S. and & Clarke, R. “Application of metabolomics in drug resistant breast cancer research.” Metabolites, 5: 100-118, 2015.
  4. Chen, X., Jung, J.-G., Shajahan-Haq, A., Clarke, R., Shih, I.-E., Wang, Y., Luca, M., Wang, T.L. & Xuan, J. “ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles.” Nucl Acids Res, in press.
  5. Rajapaksa, G., Nikolos, F., Bado, I., Clarke, R., Gustafsson, J-Å. & Thomas, C. “ERβ decreases breast cancer cell survival by regulating the IRE1/XBP-1 pathway.” Oncogene, 34: 4130-4141, 2015.
  6. Tavassoly, I., Shajahan, A., Baumann, W.T., Clarke, R. & Tyson, J.J. “Dynamical modeling of the interaction between autophagy and apoptosis in mammalian cells.” CPT: Pharmacometrics & Systems Pharmacology, 4: 263-272, 2015.
  7. Fu, Y., Yu, G., Levine, D.A., Wang, N., Shih, I.M., Zhang, Z. Clarke, R. & Wang, Y. “BACOM 2.0 facilitates absolute normalization and quantification of somatic copy number alterations in heterogeneous tumors.” Scientific Reports, 5: doi:10.1038/srep13955, 2015.
  8. Wang, N., Hoffman, E.P., Chen, L., Chen, L., Zhang, Z., Liu, C., Yu, G., Herrington, D.M., Clarke, R. & Wang, Y. “Mathematical modeling of transcriptional heterogeneity identifies novel markers and subpopulations in complex tissues.” Scientific Reports, in press.
  9. Ma, Y., Preet, A., Tomita, Y, Oliveira, E., Clarke, R., Brown, M. & Rosen, E. “A new class of small molecule estrogen receptor-alpha antagonists that overcome anti-estrogen resistance.” Oncotarget, in press.
  10. Dabydeen, S.A., Kang, K., Díaz-Cruz, E.,S., Alamri, A., Axelrod, M.L., Bouker, K.B., Al-Kharboosh, R., Clarke, R., Hennighausen, L. & Furth, P.A. “Comparison of tamoxifen and letrozole response in mammary preneoplasia of ER and aromatase over-expressing mice defines an immune-associated gene signature linked to tamoxifen resistance.” Carcinogenesis, 36: 122-132, 2015.
  11. Tian, Y., Zhang, B., Hoffman, E.R., Clarke, R., Zhang, Z., Shih, I.-E., Xuan, J., Herrington, D.M. & Wang, Y. “kDDN: An open-source Cytoscape application for constructing differential dependency networks with significant rewiring.” Bioinformatics, 31: 287-289, 2015.
  12. Wang, N., Gong, T., Clarke, R., Chen, L., Shih, I-M., Zhang, Z., Levine, D., Xuan, J. & Wang, Y. “UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples.” Bioinformatics, 31: 137-139, 2015.
  13. Xu, S., Barnes, R.O., Chen, L., Shajahan-Haq, A.N., Hilakivi-Clarke, L.A., Clarke, R., Wang, Y. & Xuan, J. “BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method.” Bioinformatics, 31:2412-2414, 2015.
  14. Sengupta, S., Biarnes, M.C., Clarke, R. & Jordan, V.C. “Inhibition of BET proteins impair estrogen mediated growth and transcription in breast cancers by pausing RNA polymerase advancement.” Breast Cancer Res Treat, 150: 265-278, 2015.
  15. Sakabe, I., Hu, R., Jin, L., Clarke, R. & Kasid, U.N. “TMEM33: A new stress-inducible endoplasmic reticulum transmembrane protein and modulator of the unfolded protein response signaling.” Breast Cancer Res Treat, 153: 285-2976, 2015.
  16. Clarke, R., Tyson, J.J. & Dixon, J.M. “Endocrine resistance in breast cancer – an overview and update.” Mol Cell Endocrinol, 418: 220-234, 2015.
  17. Shi, X., Wang, X., Shajahan, A., Hilakivi-Clarke, L., Clarke, R. & Xuan, J. “BMRF-MI: integrative identification of protein interaction network by modeling the gene dependency,” BMC Genomics, 16(Suppl 7):S10 (doi:10.1186/1471-2164-16-S7-S10), 2015.
  18. Hu, R., Hilakivi-Clarke, L. & Clarke, R. “Molecular mechanism for tamoxifen associated endometrial cancer,” Oncol Lett, 9: 1495-1501, 2015.
  19. Cook, K.L. & Clarke, R. “Role of GRP78 in promoting therapeutic-resistant breast cancer.” Future Med Chem, 7: 1529-1534, 2015.
  20. Cook, K.L. & Clarke, R. “Overcoming cancer resistance.” Future Med Chem, 7: 1471, 2015.
  21. Clarke, R. & Cook, K.L. “Unfolding the role of stress response signaling in endocrine resistant breast cancers.” Front Oncol, 5: 140, 2015; doi:10.3389/fonc.2015.00140 (10 pages as published online).
  22. Cook, K.L., Schwartz-Robert, J.L., Baumann, W.T. & Clarke, R. “Linking autophagy with inflammation through interferon regulatory factor-1 signaling in ER+ breast cancer.” Mol Cell Oncol, 2015 doi:10.1080/23723556.2015.1023928 (3 pages as published online).
  23. Raghavan, K.S., Shajahan, A. and & Clarke, R. “Integrating proteotoxic stress response pathways for induction of cell death in cancer cells: molecular mechanisms and therapeutic opportunities. In: Stress Response Pathways in Cancer, Springer Science, Ed. Wondrak, G.T. pp 183-202, 2015.
  24. Clarke, R., Crook, E. & Federoff, H.J. “Chapter 14: The changing spectrum of biomedical and clinical research.” In “The Transformation of Academic Health Centers,” Ed. Wartman, S.A. Academic Press, pp137-148, 2015.
  25. Tran, A.T., Ramalinga, M., Kedir, H., Clarke, R. & Kumar, D. “Autophagy inhibitor 3-methyladenine potentiates apoptosis induced by dietary tocotrienols in breast cancer cells.” Eur J Nutr, 54: 265-272, 2015.

Year 2014
  1. Shajahan-Haq, A.N., Cook, K.L. Schwartz-Robert, J.L., Eltayeb, A.E., Demas, D.M., Facey, C.B.O., Wärri, A., Hilakivi-Clarke, L.A. & Clarke, R. “MYC regulates the unfolded protein response and glucose and glutamine uptake in endocrine resistant breast cancer.” Molecular Cancer, 13: 239 (doi:10.1186/1476-4598-13-239), 2014.
  2. Figg, W., Shajahan, A.N. & Clarke, R. “Aromatase inhibitor plus ovarian suppression as adjuvant therapy in premenopausal women with breast cancer.” Cancer Biol Ther, 15: 1586-1587, 2014.
  3. Madhavan, S., Gauba, R., Clarke, R. & Gusev, Y. “Integrative knowledge-driven analysis pipeline for untargeted metabolomics.” Metabolomics, 4:1, doi: 10.4172/2153-0769.1000130 (11 pages as published online), 2014.
  4. Gu, J., Wang, X., Hilakivi-Clarke, L., Clarke, R. & Xuan J. "BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data," BMC Bioinformatics (Suppl - Proceedings of RECOMB-seq 2014) 15 (suppl 9):S6 doi:10.1186/1471-2105-15-S9-S6, 2014.
  5. Chen, X., Shi, X., Shajahan, A., Hilakivi-Clarke, L., Clarke, R. & Jianhua Xuan. “BSSV: Bayesian based somatic structural variation identification with whole genome DNA-Seq data.” Conf Proc 36th Annual International IEEE Eng Med Biol Soc Conference, pp 3837-3940, 2014.
  6. Brouxhon, S.M., Kyrkanides, S., Teng, X., O’Banion, M.K., Clarke, R., Byers, S. & Ma, L. “Soluble E-cadherin activates HER and IAP family members HER2+ and TNBC human breast cancers.” Mol Carcinog, 53: 893-906, 2014.
  7. Yu, G., Zhang, B., Hu, X., Yuan, X., Shih, L.-M., Zhang, Z., Clarke, R., Roger, R.W., Fu, Y., Wang, Y. “AISAIC: a software suite for accurate identification of significant aberrations in cancers.” Bioinformatics, 30: 431-433, 2014.
  8. Chen, L., Choyke, P.L., Wang, N. Clarke, R., Bhujwalla, Z.M., Hillman, E.M.C., Wang, G. & Wang, Y. “Unsupervised deconvolution of dynamic imaging reveals intratumor vascular heterogeneity and repopulation dynamics,” PLoS ONE, 9(11): (doi:10.1371/journal.pone. 0112143), 2014.
  9. Ma, Y., Tomita, Y, Preet, A., Clarke, R., Englund, E., Grindrod, S., Oliveira, E., Brown, M. & Rosen, E. “Small molecule “BRCA1-mimetics” are antagonists of estrogen receptor-alpha.” Mol Endocrinol, 28: 1971-1986, 2014.
  10. Tian, Y., Wang, S.S., Zhang, Z., Rodriguez, O.C., Petrocoin, E., Shih, I.-E., Chan, D., Avantaggiati, M., Yu, G., Ye, S., Clarke, R., Wang, C., Zhang, B. & Albanese, C. “Integration of network biology and imaging to study cancer phenotypes and responses.” IEEE/ACM Trans Computational Biol Bioinformatics, 11:1009-1019, 2014.
  11. Cook, K.L. & Clarke, R. “Estrogen receptor-α signaling and localization regulates autophagy and unfolded protein response activation in ER+ breast cancer.” Receptors Clin Investig, 1: e316; (doi: 10.14800/rci.316), 2014.
  12. Tian Y, Zhang B, Hoffman EP, Clarke R, Zhang Z, Shih IM, Xuan J, Herrington DM, Wang Y. Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks. BMC Syst Biol. 2014 Jul 24;8(1):87. PubMed
  13. Hatzis C, Bedard PL, Birkbak NJ, Beck AH, Aerts HJ, Stern DF, Shi L, Clarke R, Quackenbush J, Haibe-Kains B. Enhancing Reproducibility in Cancer Drug Screening: How Do We Move Forward? Cancer Res. 2014 Aug 1;74(15):4016-4023. Epub 2014 Jul 11. PubMed
  14. Chen C, Baumann WT, Xing J, Xu L, Clarke R, Tyson JJ., Mathematical models of the transitions between endocrine therapy responsive and resistant states in breast cancer. Interface Focus. 2014 May 7;11(96):20140206. doi: 10.1098/rsif.2014.0206. Print 2014 Jul 6. PubMed
  15. Cook KL, Wärri A, Soto-Pantoja DR, Clarke PA, Cruz MI, Zwart A, Clarke R. Hydroxychloroquine inhibits autophagy to potentiate antiestrogen responsiveness in ER+ breast cancer. Clin Cancer Res. 2014 Jun 15;20(12):3222-32. doi: 10.1158/1078-0432.CCR-13-3227. PubMed
  16. Aguilar H, Urruticoechea A, Halonen P, Kiyotani K, Mushiroda T, Barril X, Serra-Musach J, Islam A, Caizzi L, Di Croce L, Nevedomskaya E, Zwart W, Bostner J, Karlsson E, Pérez Tenorio G, Fornander T, Sgroi DC, Garcia-Mata R, Jansen MP, García N, Bonifaci N, Climent F, Soler MT, Rodríguez-Vida A, Gil M, Brunet J, Martrat G, Gómez-Baldó L, Extremera AI, Figueras A, Balart J, Clarke R, Burnstein KL, Carlson KE, Katzenellenbogen JA, Vizoso M, Esteller M, Villanueva A, Rodríguez-Peña AB, Bustelo XR, Nakamura Y, Zembutsu H, Stål O, Beijersbergen RL, Pujana MA. VAV3 mediates resistance to breast cancer endocrine therapy. Breast Cancer Res. 2014 May 28;16(3):R53. doi: 10.1186/bcr3664. PubMed
  17. Cook KL, Clarke PA, Parmar J, Hu R, Schwartz-Roberts JL, Abu-Asab M, Wärri A, Baumann WT, Clarke R. Knockdown of estrogen receptor-α induces autophagy and inhibits antiestrogen-mediated unfolded protein response activation, promoting ROS-induced breast cancer cell death. FASEB J. 2014 May 23. pii: fj.13-247353. PubMed
  18. Tran AT, Ramalinga M, Kedir H, Clarke R, Kumar D.Autophagy inhibitor 3-methyladenine potentiates apoptosis induced by dietary tocotrienols in breast cancer cells.Eur J Nutr. 2014 May 16. PubMed
  19. Cook KL, Soto-Pantoja DR, Abu-Asab M, Clarke PA, Roberts DD, Clarke R. Mitochondria directly donate their membrane to form autophagosomes during a novel mechanism of parkin-associated mitophagy. Cell Biosci. 2014 Mar 27;4(1):16. doi: 10.1186/2045-3701-4-16. PubMed
  20. Zhang B, Hou X, Yuan X, Shih IeM, Zhang Z, Clarke R, Wang RR, Fu Y, Madhavan S, Wang Y, Yu G. AISAIC: a software suite for accurate identification of significant aberrations in cancers. Bioinformatics. 2014 Feb 1;30(3):431-3. doi: 10.1093/bioinformatics/btt693. Epub 2013 Nov 29. PubMed

Year 2013
  1. Shi X, Gu J, Chen X, Shajahan A, Hilakivi-Clarke L, Clarke R, Xuan J. mAPC-GibbsOS: an integrated approach for robust identification of gene regulatory networks. BMC Syst Biol. 2013;7 Suppl 5:S4. doi: 10.1186/1752-0509-7-S5-S4. Epub 2013 Dec 9. PubMed
  2. Chen C, Baumann WT, Clarke R, Tyson JJ. Modeling the estrogen receptor to growth factor receptor signaling switch in human breast cancer cells. FEBS Lett. 2013 Oct 11;587(20):3327-34. doi: 10.1016/j.febslet.2013.08.022. Epub 2013 Aug 28. PubMed
  3. Parmar JH, Cook KL, Shajahan-Haq AN, Clarke PA, Tavassoly I, Clarke R, Tyson JJ, Baumann WT. Modelling the effect of GRP78 on anti-oestrogen sensitivity and resistance in breast cancer. Interface Focus. 2013 Aug 6;3(4):20130012. doi: 10.1098/rsfs.2013.0012. PubMed
  4. Chen X, Xuan J, Wang C, Shajahan AN, Riggins RB, Clarke R. Reconstruction of transcriptional regulatory networks by stability-based network component analysis. IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov-Dec;10(6):1347-58. doi: 10.1109/TCBB.2012.146. PubMed
  5. Cook KL, Clarke PA, Clarke R. Targeting GRP78 and antiestrogen resistance in breast cancer.Future Med Chem. 2013 Jun;5(9):1047-57. doi: 10.4155/fmc.13.77. Review. PubMed
  6. Schwartz-Roberts JL, Shajahan AN, Cook KL, Wärri A, Abu-Asab M, Clarke R. GX15-070 (obatoclax) induces apoptosis and inhibits cathepsin D- and L-mediated autophagosomal lysis in antiestrogen-resistant breast cancer cells. Mol Cancer Ther. 2013 Apr;12(4):448-59. doi: 10.1158/1535-7163.MCT-12-0617. Epub 2013 Feb 8.  PubMed
  7. Gusev, Y., Riggins, R.B., Bhuvaneshwar, K., Gauba, R., Clarke, R. & Madhavan, S. In silico discovery of mitotic regulation networks associated with early distant metastases in ER+ breast cancers, Cancer Informatics, 12: 31-51, 2013. PubMed
  8. Bouker, K.B., Wang, Y., Xuan, J. & Clarke, R. Antiestrogen resistance and the application of systems biology Drug Discov Today Dis Mech, in press, 2013.
  9. Abu-Asab, M., Abu-Asab, N., Loffredi, C. Clarke, R. & Amri, H. Identifying early events of gene expression in breast cancer with systems biology phylogenetics. Cytogenet Genome Res, in press, 2013.
  10. Hou, X., Yu, G., Zhang, B., Shih, I.-M., Zhang, Z., Yuan, X., Clarke, R. & Madhavan, S. Accurate identification of significance aberrations in contaminated cancer genome. Proc 2012 IEEE Intl Workshop Genomic Signal Processing Stats (GENSIPS), in press, 2013.
  11. Clarke, R. & Jordan, V.C. Antihormone drug resistance. In: “Estrogen Action and Women's Health,” Eds: Jordan, V.C., World Scientific, Singapore; in press, 2013.

Year 2012
  1. Clarke, R., Cook, K.L., Hu, R., Facey, C.O.B., Tavassoly, I., Schwartz, J., Baumann, W.T., Tyson, J.J., Xuan, J., Wang, Y., Wärri, A. & Shajahan, A.N. Endoplasmic reticulum stress, the unfolded protein response, autophagy, and the integrated regulation of breast cancer cell fate. Cancer Res, 72:1321-1331, 2012. PubMed
  2. Cook, K.L., Shajahan, A.N., Jin, L., Wärri, A., Hilakivi-Clarke, L.A. & Clarke, R. The unfolded protein response regulator GRP78 controls crosstalk between apoptosis and autophagy to determine antiestrogen responsiveness. Cancer Res, 72: 3337-3349, 2012. PubMed
  3. Shajahan, A.N., Dobbin, Z.C., Hickman, F.E., Dakshanamurthy, S. & Clarke, R. Phosphorylated caveolin-1 (Y14) sensitizes breast cancer cells to paclitaxel by JNK-mediated inhibition of BCL2/BCLxL. J Biol Chem, 287: 17682-17692, 2012. PubMed
  4. Chen, L., Xuan, J., Riggins, R.B., Wang, Y. & Clarke, R. Identifying protein interaction subnetworks by a bagging Markov random field-based method. Nucleic Acid Res, 2013 Jan;41(2):e42. doi: 10.1093/nar/gks951. Epub 2012 Nov 17. PubMed
  5. Gu, J., Xuan, J., Riggins, R.B., Chen, L., Wang Y. & Clarke, R. Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic. Bioinformatics, 28: 1990-1997, 2012. PubMed
  6. Klionsky, D.J., Abdalla, F.C., Abeliovich, H., Abraham, R.T., Clarke, R., Zschocke, J. & Zuckerbraun, B. (this project was led by Dr. Klionsky and the paper has too many authors to list all here; authors are listed alphabetically by surname). Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy, 8: 445-544, 2012. PubMed
  7. Cook, K.L. & Clarke, R. Glucose-regulated protein 78 AMPing up autophagy. Autophagy, in press, 2012. PubMed
  8. Woode, D.R., Aiyer, H.S., Sie, N., Zwart, A., Li, L., Seeram, N.P. & Clarke, R. Effect of berry extracts and bioactive compounds on Fulvestrant (ICI 182,780) sensitive and resistant cell lines. Int J Breast Cancer, doi:10.1155/2012/147828 (11 pages as published online), 2012. PubMed
  9. Aiyer, H., Wärri, A., Woode, D., Hilakivi-Clarke, L.A. & Clarke, R. Influence of berry polyphenols on receptor signaling and cell-death pathways: implications for breast cancer prevention. J Agric Food Chem, 60: 5693-5708, 2012. PubMed
  10. Yuan, X., Yu, G., Hou, X., Shih, I.-M., Clarke, R., Zhang, J., Hoffman, E.P., Wang, R.R., Zhang, Z. & Wang, Y. Genome-wide identification of significant aberrations in cancer genomes. BMC Genomics, 13: 342, 2012 (doi:10.1186/1471-2164-13-342; 14 pages as published online). PubMed
  11. Wang, C., Xuan, J., Shih, I.-M., Clarke, R. & Wang, Y. Regulatory component analysis: a semi-blind extraction approach to infer gene regulatory networks with imperfect biological knowledge. Signal Process, 92: 1902-1915, 2012. PubMed
  12. Aiyer, H., Bouker, K.B., Cook, K.L., Facey, C.O.B., Hu, R., Schwartz, J., Shajahan, A.N., Hilakivi-Clarke, L.A. & Clarke, R. Interaction of dietary polyphenols with molecular signaling pathways of antiestrogen resistance: possible role in breast cancer recurrence. Hormone Mol Biol Clin Invest, in press, 2012.
  13. Chen, X., Wang, C., Shajahan, A.N., Riggins, R.B., Clarke, R. & Xuan, J. Reconstruction of transcription regulatory networks by stability-based network component analysis, Lecture Notes Comp Sci, 7292: 36-47, 2012. PubMed
  14. Patacsil, D., Osayi, S., Tran, A.T., Saenz, F., Yimer, L., Shajahan, A.N., Gokhale, P.G., Verma, M., Clarke, R., Chauhan, S.C. & Kumar, D. Vitamin E succinate inhibits survivin and induces apoptosis in pancreatic cancer cells. Genes Nutr, 7: 83-89, 2012. PubMed

Year 2011
  1. Ren, Z., Wang, Y., Tao, D., Liebenson, D., Liggett, T., Goswami, R., Clarke, R., Stefoski, D. & Balabanov, R. Overexpression of the dominant negative form of IRF1 in oligodendrocytes protects against experimental autoimmune encephalomyelitis. J Neurosci, 31: 8329-8341, 2011. PubMed
  2. Schwartz, J., Shajahan, A.N. & Clarke, R. The role of interferon regulatory factor-1 (IRF1) in Overcoming antiestrogen resistance in the treatment of breast cancer. Int J Breast Cancer, 2011:912102, 2011. PubMed
  3. McCarver, G., Bhatia, J., Chambers, C., Clarke, R., Etzel, R., Foster, W., Hoyer, P., Leeder, J.S., Peters, J., Rissman, E., Rybak, M., Sherman, C., Toppari, J. & Turner, K. NTP-CERHR expert panel report on the developmental toxicity of soy infant formula. Birth Defects Res B Dev Reprod Toxicol 92: 421-468, 2011. PubMed
  4. Zhang, Y., Xuan, J., Clarke, R. & Ressom, H. Module-based breast cancer classification. Int J Data Mining Bioinformatics, in press, 2011.
  5. Tyson, J.J., Baumann, W.T., Chen, C., Verdugo, A., Tavassoly, I., Wang, Y., Weiner, L.M. & Clarke, R. Dynamic models of estrogen signaling and cell fate in breast cancer cells. Nature Rev Cancer, 11: 523-532, 2011. Nature Reviews
  6. Zhang, B., Tian, Y., Jin, L., Li, H., Shih, I.-M., Madhavan, S., Clarke, R., Hoffman, E.P., Xuan, J., Hilakivi-Clarke, L. & Wang, Y. DDN: a caBIGTM analytical tool for differential network analysis. Bioinformatics, 27: 1036-1038, 2011. PubMed
  7. Yu, G., Li, H., Ha, S., Shih, I.-M., Clarke, R., Hoffman, E.P., Madhavan, S., Xuan, J. & Wang, Y. PUGSVM: a caBIGTM analytical tool for multiclass gene selection and predictive classification. Bioinformatics, 27: 736-738, 2011. PubMed
  8. Gong, T., Xuan, J., Chen, L., Riggins, R.B., Li, H., Hoffman, E.P., Clarke, R. & Wang, Y. Motif-guided sparse decomposition of gene expression data for regulatory module identification. BMC Bioinformatics, 12:82 (doi:10.1186/1471-2105-12-82; 16 pages as published on-line), 2011. PubMed
  9. Chen, L., Xuan, J., Riggins, R.B., Clarke, R. & Wang, Y. Identifying cancer biomarkers by network-constrained support vector machines. BMC Syst Biol, 5: 161 (doi:10.1186/1752-0509-5-161; 20 pages as published on-line), 2011. PubMed
  10. Madhavan., S., Gusev, Y., Harris, M., Tanenbaum, D.M., Gauba, R., Bhuvaneshwar, K., Shinohara, A., Rosso, K., Carabet, L.A., Song, S., Riggins, R.B., Dakshanamurthyu, S., Wang, Y., Byers, S.W., Clarke, R. & Weiner, L.M. G-DOC®: a systems medicine platform for personalized oncology. Neoplasia 13: 771-783, 2011. PubMed
  11. Clarke, R., Shajahan, A.N., Wang, Y., Tyson, J.J. Riggins, R.B. Weiner, L.M., Bauman, W.T., Xuan, J., Zhang, B., Facey, C., Aiyer, H., Cook, K., Hickman, E.F., Tavassoly, I., Verdugo, A., Chen, C., Zwart, A., Wärri, A., Hilakivi-Clarke, L.A. “Endoplasmic reticulum stress, the unfolded protein response, and gene network modeling in antiestrogen resistant breast cancer.” Hormone Mol Biol Clin Invest, 5: 35-44, 2011. Hormone Molecular Biology and Clinical Investigation
  12. Thangavel, C., Dean, J., Ertel, A., Knudsen, K., Aldaz, M., Clarke, R. & Knudsen, E. Therapeutically activating RB: reestablishing cell cycle control in endocrine therapy resistant breast cancer. Endocr-Relat Cancer, 18: 333-345, 2011. PubMed
  13. Clarke, R. Cannibalism, cell survival, and endocrine resistance in breast cancer. Breast Cancer Res, 13: 311 (3 pages as published on-line), 2011. PubMed
  14. Cook, K.L., Shajahan, A.N. & Clarke, R. Autophagy and endocrine resistance in breast cancer. Expert Rev Anticancer Ther, 11: 1283-1294, 2011. PubMed
  15. Patacsil, D., Tran, A.T., Cho, Y.S., Suy, S., Saenz, F., Malyukova, I., Ressom, H. Collins, S.P., Clarke, R. & Kumar, D. Gamma-Tocotrienol induced apoptosis is associated with the unfolded protein response in human breast cancer cells. J Nutr Biochem, in press. PubMed

Year 2010
  1. Zhang, Y., Xuan., J., Clarke, R. & Ressom, H.W. “Module-based biomarker discovery in breast cancer metastasis.” Proc IEEE Intl Conf Bioinformatics Biomedicine (BIBM 2010), in press.
  2. Wang, C., Xuan, J., Li, H., Wang, Y., Zhan, M., Hoffman, E.P. & Clarke, R. “Knowledge-guided gene ranking by coordinative component analysis.” BMC Bioinformatics, 11:162, 2010 (13 pages as published on-line) BMC Bioinformatics
  3. Yu, G., Feng, Y., Miller, D.J., Xuan, J., Hoffman, E.P., Clarke, R. & Wang, Y. “Matched gene selection and committee classifier for molecular classification of heterogeneous diseases.” J Mach Learn Res, 11: 2141-2167, 2010. Journal of Machine Learning Research
  4. Broustas, C.G., Ross, J.S., Yang, Q., Sheehan, C.E., Riggins, R.B., Cavalli, L.R., Haddad, B.R., Seillier-Moiseiwitsch, F., Kallakury, B.V.S., Haffty, B.G., Clarke, R. & Kasid, U.N. “The pro-apoptotic molecule BLID interacts with BCL-XL and its downregulation in breast cancer correlates with poor disease free and overall survival.” Clin Cancer Res, 16:2939-48, 2010. PubMed
  5. Zhang, Y., Xuan, J., de los Reyes, B.G., Clarke, R. & Ressom, H.W. “Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration.” PLoS ONE, 5 (4): e10268, 2010. PubMed
  6. Nehra, R., Riggins, R.B., Shajahan, A.N., Zwart, A., Crawford, A.C. & Clarke, R. “BCL2 and CASP8 regulation by NFκB affect mitochondrial function and cell fate in antiestrogen sensitive and resistant breast cancer cells.” FASEB J, 24: 2039-2054, 2010. PubMed
  7. Ning, Y. Riggins, R.B., Mulla, J.E., Chung, H., Zwart, A. & Clarke, R. “IRF1 is required for the reversal of antiestrogen resistance by interferon-gamma.” Mol Cancer Ther, 9: 1274-1285, 2010.
  8. Crawford, A.C., Riggins, R.B., Shajahan, A.N., Zwart, A., & Clarke, R. “BCL-W and BCL2 are key regulators of apoptotic, necrotic and autophagic cell fate decisions in response to antiestrogens.” PLoS ONE, 5 (1): e8604, 2010. PubMed
  9. Chen, L., Xuan, J., Riggins, R.B., Wang, Y., Hoffman, E.P. & Clarke, R. “Multi-level support vector regression analysis to identify condition-specific regulatory networks.” Bioinformatics, 26: 1426-1422, 2010. Bioinformatics
  10. Shajahan, A.N., Goel, S., de Assis, S., Yu, B., Clarke, R. & Hilakivi-Clarke, L.A. “Changes in mammary caveolin-1 signaling pathways are associated with breast cancer risk in rats exposed to estradiol in utero or during prepuberty.” Hormone Mol Biol Clin Invest, in press.
  11. Wang, C., Xuan, J., Li, H., Wang, Y., Zhan, M., Hoffman, E.P. & Clarke, R. “Knowledge-guided gene ranking by coordinative component analysis.” BMC Bioinformatics, 11:162, 2010 (13 pages as published on-line). BMC Bioinformatics
  12. Trauernicht, A.M., Kim, S.J., Kim, N.H., Clarke, R. & Boyer, T.G. “DBC-1 mediated endocrine resistance in breast cancer cell survival.” Cell Cycle, 9: 1218-1219, 2010. PubMed
  13. Xuan, J., Wang, Y., Hoffman, E. & Clarke, R. “Cross phenotype normalization of microarray data.” Front Biosci, E2: 171-186, 2010. PubMed
  14. Zhang, B., Li, H., Clarke, R. & Wang, Y. “Differential dependency network analysis to identify topological rewiring in biological networks.” In: Medical Biostatistics for Complex Diseases. Eds. Emmert-Streib, F. & Dehmer, M., Wiley-VCH, Berlin, Germany, pp185-203, 2010.

Year 2009
  1. Shajahan, A.N., Riggins, R.B. & Clarke, R. “The role of X-box binding protein-1 in tumorigenicity” Drug News Perspect 22: 241-246, 2009. PubMed
  2. Clarke, R. “The role of preclinical animal models in breast cancer drug development.” Breast Cancer Research, 11(Suppl 3):S22, 2009. PubMed
  3. Chen, L., Xuan, J., Wang, C., Shih, L.-M., Wang, T.-L., Zhang, Z., Clarke, R., Hoffman, E.P. & Wang, Y. “Biomarker identification by knowledge driven multilevel ICA and motif analysis.” Int J Data Mining Bioinformatics, 3: 365-381, 2009. PubMed
  4. Zhang, Y., Xuan, J., de los Reys, B.G., Clarke, R. & Ressom, H.W. “Reverse engineering module networks by PSO-RNN hybrid modeling.” BMC Genomics, 10:S15 (10 pages as published on-line), 2009. PubMed
  5. Zhang, B., Li, H., Riggins, R.B., Zhan, M., Xuan, J., Zhang, Z., Hoffman, E.P., Clarke, R. & Wang, Y. “Differential dependency network analysis to identify condition-specific topological changes in biological networks.” Bioinformatics, 25: 526-532, 2009.PubMed
  6. Cavalli, L.R., Riggins, R.B., Wang, A., Clarke, R.*, & Haddad, B.R. “Frequent loss of heterozygosity at the interferon regulatory factor-1 (IRF1) gene locus in breast cancer” Breast Cancer Res Treat, 121: 227-231, 2010. *corresponding author PubMed
  7. Clarke, R., Shajahan, A.N., Riggins, R.B., Cho, Y., Crawford, A., Xuan, J., Wang, Y., Zwart, A., Nehra, R. & Liu, M.C. “Gene network signaling in hormone responsiveness modifies apoptosis and autophagy in breast cancer cells.” J Steroid Biochem Mol Biol, 114: 8-20, 2009. PubMed
  8. Clarke, R., Shajahan, A.N., Riggins, R.B., Cho, Y., Crawford, A., Xuan, J., Wang, Y., Zwart, A., Nehra, R. & Liu, M.C. “Gene Network signaling in hormone responsiveness modifies apoptosis and autophagy in breast cancer cells.” J Steroid Biochem Mol Biol, 114:8-20, 2009. PubMed
  9. Xuan, J., Wang, Y., Hoffman, E., Clarke, R., “Cross phenotype normalization of microarray data.” Front Biosci, in press, 2009.
  10. Chen, L. Xuan, J., Riggins, R.B., Wang, Y. Hoffman, E.P., & Clarke, R., “Identification of condition-specific regulatory modules through multi-level motif and mRNA expression analysis,” Int J Comp Biology Drug Design, in press, 2009. InderScience
  11. Clarke, R., Shajahan, A.N., Riggins, R.B., Cho, Y., Crawford, A., Xuan, J., Wang, Y., Zwart, A., Nehra, R. & Liu, M.C. “Gene network signaling in hormone responsiveness modifies apoptosis and autophagy in breast cancer cells.” J Steroid Biochem Mol Biol, 114: 8-20, 2009. PubMed
  12. Zhang, B., Li, H., Riggins, R.B., Zhan, M., Xuan, J., Zhang, Z., Hoffman, E.P., Clarke, R., Wang, Y., “Differential dependency network analysis to identify condition-specific topological changes in biological networks” Bioinformatics, 25: 526-532, 2009. PubMed
  13. Chen, L., Xuan, J., Wang, C., Shih, L.-M., Wang, T.-L., Zhang, Z., Clarke, R., Hoffman, E.P. & Wang, Y., “Biomarker identification by knowledge driven multilevel ICA and motif analysis.” Int J Data Mining Bioinformatics, 3: 363-379, 2009. IEEE

Year 2008
  1. Olivo, S., Zhu, Y., Lee, R.Y., Cabanes, A., Khan, G., Zwart, A., Wang, Y, Clarke, R., Hilakivi-Clarke, L.A., “Identification of gene signaling pathways mediating the opposite effects of prepubertal low and high fat n-3 PUFA diets on breast cancer risk.” Cancer Prev Res, 1: 522-531, 2008. PubMed
  2. Chen, L., Xuan, J., Wang, C., Shih, L-M., Wang, Y., Zhang, Z., Hoffman, E.P., Clarke, R., “Knowledge-guided multi-scale independent component analysis for biomarker identification.” BMC Bioinformatics, 9:416 (16 pages as published on-line), 2008. PubMed
  3. Zhu, Y., Li, H., Miller, D., Wang, Z., Xuan, J., Clarke, R., Hoffman, E.P. & Wang, Y., “caBIG VISDA: modeling, visualization and discovery for cluster analysis of genomic data.” BMC Bioinformatics, 9: 383 (18 pages as published on-line), 2008. PubMed
  4. Chen, L., Xuan, J., Wang, Y., Riggins, R.B., Clarke, R. “Network-constrained support vector machine for classification.” 7th Intl Conf Machine Learning Applications (IMCLA), 60-65, 2008. IEEE
  5. Deb, T.B., Ramlijak, D., Dickson, R.B., Johnson, M.D. & Clarke, R. “Signaling pathways in the normal and neoplastic breast.” In: “Handbook of Cell Signaling.” Eds: Thompson, B.E.; Elsevier, Inc. New York, NY; in press.
  6. Zhang, Y., Xuan, J., de los Reyes, B.G., Clarke, R. & Ressom, H.W. ”Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data.” BMC Bioinformatics, 9:203 (18 pages as published on-line), 2008. PubMed
  7. Wang, C., Xuan, J., Chen, L., Zhao, P., Wang, Y., Clarke, R., Eric Hoffman, E. “Integrative network component analysis for regulatory network reconstruction.” Proc. 4th Intl Symp Bioinformatics Res Applications (ISBRA), in press, 2008. SpringerLink
  8. Shajahan, A.N., Riggins, R.B. & Clarke, R. “Apoptosis, cell death and breast cancer” Chapter 8. In: “Breast cancer: prognosis, treatment, and prevention.” Eds: Pasqualini, J.R., Informa Healthcare; New York, NY; pp137-156, 2008.
  9. Wang, Y., Miller, D.J. & Clarke, R. “Approaches to working in high dimensional data spaces: gene expression microarrays.” Br J Cancer, 98: 1023-1028, 2008. PubMed
  10. Zhu, Y., Wang, Z., Miller, D.J., Clarke, R., Xuan, J., Hoffman, E.P. & Wang, Y. “A ground truth based comparative study on clustering of gene expression data.” Front Biosci, 13: 3839-3849, 2008. PubMed
  11. Riggins, R.B., Lan, P.-J., Klimach, U., Zwart, A., Cavalli, L.R., Haddad, B.R, Chen, L., Xuan, J., Ethier, S.P. & Clarke, R. “ERRγ mediates Tamoxifen resistance in a novel model of invasive lobular breast carcinoma.” Cancer Res, 68: 8908-8917, 2008. PubMed
  12. Clarke, R., Ressom, H., Wang, A., Xuan, J., Liu, M.C., Gehan, E. & Wang, Y. “The properties of high-dimensional data spaces: implications for exploring gene and protein expression data.” Nature Rev Cancer, 8: 37-49, 2008. PubMed
  13. Wang, C., Chen, L., Zhao, P., Hoffman, E., Clarke, R., Wang, Y. & Xuan, J. “Motif-directed component analysis for regulatory network inference.” BMC Bioinformatics, 9: S21 (9 pages as published on-line), 2008. PubMed
  14. Ressom, H.W., Varghese, R.S., Zhang, Z., Xuan, J. & Clarke, R. “Classification algorithms for phenotype prediction in genomics and proteomics.” Front Biosci, 13: 691-708, 2008. PubMed

Year 2007
  1. Gomez, B.P. Riggins, R.B., Shajahan A., Klimach, U., Zhu, Y., Zwart, A., Wang, M., Wang, A. & Clarke, R. “Human X-box binding protein-1 confers both estrogen-independence and antiestrogen resistance in breast cancer.” FASEB J, 21:4013-27, 2007. PubMed
  2. Naughton, C., Kuske, B., MacLeod, K., Clarke, R. Cameron, D.A. & Langdon, S.P. “Progressive loss of estrogen receptor alpha (ERα) cofactor recruitment in endocrine resistance.” Mol Endocrinol, 21:2615-26, 2007. PubMed
  3. Gong, T., Xuan, J., Wang, C., Li, H., Hoffman, E., Clarke, R. & Wang, Y. “Gene module identification from microarray data using nonnegative independent component analysis.” Gene Regulat Sys Biol, 1: 349-363, 2007. Gene Regulat Sys Biol
  4. Xuan, J., Wang, Y., Dong, Y., Feng, Y., Wang, B., Khan, J., Bakay, M., Wang, Z., Pachman, L., Winokur, S., Chen, Y.-W., Clarke, R., & Hoffman E. “Gene selection for multiclass prediction by weighted Fisher criterion.” EURASIP J Bioinformat System Biol, 2007: Article ID 64628, 15 pages, 2007. PubMed
  5. Xuan, J., Wang, Y., Clarke, R. & Hoffman, E., “An iterative nonlinear regression method for microarray data normalization,” Open Appl Informatics J, 1: 11-19, 2007.
  6. Wang, J., Li, H., Zhu, Y., Yousef, M., Mebozhyn, M., Showe, N., Xuan, J., Clarke, R. & Wang, Y. “VISDA: an open-source caBIGTManalytical tool for data clustering and beyond.” Bioinformatics, 23: 2024-2027, 2007. PubMed
  7. Bouker, K.B., Skaar, T.C., Harburger, D.S., Riggins, R.B., Fernandez, D.R., Zwart, A. & Clarke, R. “The A4396G polymorphism in interferon regulatory factor-1 is frequently expressed in breast cancer.” Cancer Genet Cytogenet, 175: 61-4, 2007. PubMed
  8. Shajahan, A., Wang, A., Decker, M., Minshall, R.D., Liu, M.C. & Clarke, R. “Caveolin-1 tyrosine phosphorylation (Y14) enhances paclitaxel-mediated cytotoxicity.” J Biol Chem, 282: 5934-5943, 2007. PubMed

Year 2006
  1. Trock, B.J., Hilakivi-Clarke, L.A. & Clarke, R. “Meta-analysis of soy intake and breast cancer risk.” J Natl Cancer Inst, 98: 459-471, 2006. PubMed
  2. Wang, L.H., Yang, X.Y., Zhang, X., An, P., Kim, H.-J., Huang, J., Clarke, R., Osborne, C.K., Inman, J.K., Appella, E. & Farrar, W.L. “Disruption of estrogen receptor DNA-binding domain and related intramolecular communication restores tamoxifen sensitivity in resistant breast cancer.” Cancer Cell, 10: 487-499, 2006. PubMed
  3. Ressom, H.W., Zhang, Y., Xuan, J., Wang, Y. & Clarke, R. "Inferring network interactions using recurrent neural networks and swarm intelligence," Proc 28th IEEE EMBS Intl Conf, pp. 4241-4244, 2006. PubMed
  4. Kuske, B., Naughton, C., Moore, K., MacLeod, K.G., Miller, W.R., Clarke, R. Langdon, S.P. & Cameron, D.A. “Endocrine therapy resistance can be associated with high estrogen receptor alpha (ERα) expression and reduced ERα phosphorylation in breast cancer models.” Endocr Related Cancer, 13: 1121-1133, 2006. PubMed
  5. Feng, Y., Wang, Z., Zhu, Y., Xuan, J., Miller, D., Clarke, R., Hoffman, E.P. & Wang, Y. “Learning the tree of phenotypes using genomic data and VISDA.” 6th IEEE Symp Bioinf Bioeng (BIBE´06), 165-170, 2006. ACM
  6. Gong, T., Xuan, J., Zhu, J., Li, H., Clarke, R., Hoffman, E. & Wang, Y. “Composite gene module discovery using non-negative independent component analysis.” IEEE/NLM Life Sci Sys Apps Workshop, 1-3, 2006. PubMed
  7. Ressom, H.W., Zhang, Y., Xuan, J., Wang, Y. & Clarke, R. “Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence.” IEEE Symp Compl Intel Bioinf Comput Biol, 435-442, 2006. IEEE
  8. Zhu, Y., Wang, A., Liu, M.C., Zwart, A., Lee, R.Y., Gallagher, A., Wang, Y., Miller, W.R., Dixon, J.M. & Clarke, R.“Estrogen receptor alpha (ER) positive breast tumors and breast cancer cell lines share similarities in their transcriptome data structures.” Int J Oncol, 29: 1581-1589, 2006. PubMed
  9. Riggins, R.B., Thomas, K.S., Ta, H.Q., Donelan, S.S., Owen, K.A., Gibson, M.A., Shupnik, M.A., Silva, C.M., Parsons, S.J., Clarke, R. & Bouton A.H. “Physical and functional interactions between Cas and c-Src induce tamoxifen resistance of breast cancer cells through pathways involving EGFR and STAT5b.” Cancer Res, 66: 7007-7015, 2006. PubMed
  10. Trock, B.J., Hilakivi-Clarke, L.A. & Clarke, R. “Meta-analysis of soy intake and breast cancer risk.”, J Natl Cancer Inst 98: 459-471, 2006. PubMed
  11. Wong, L.-J.C., Dai, P., Lu, J.-F., Lou, M.A., Clarke, R. & Nazarov, N. “AIB1 gene amplification and the instability of polyQ encoding sequence in breast cancer cell lines.”, BMC Cancer 6: 111-132, 2006. PubMed
  12. Wang, Z., Wang, Y., Xuan, J., Dong, Y., Bakay, M., Khan, J., Clarke, R. & Hoffman, E.P. “Optimized multilayer perceptrons for molecular classification and diagnosis using genomic data.”, Bioinformatics 22: 755-761, 2006. PubMed

Year 2005
  1. Xuan, J., Wang, Y., Clarke, R. & Hoffman, E.P. “Normalization of microarray data by iterative nonlinear regression.”, Fifth IEEE Symposium on Bioinformatics and Bioengineering, Minneapolis, Minnesota, pp. 267-270, 2005. IEEE
  2. Riggins, R.B., Bouton, A.H., Liu, M.C. & Clarke, R. “Antiestrogens, aromatase inhibitors, and apoptosis in breast cancer.”, Vit Horm 71: 202-237, 2005. PubMed
  3. Bouker, K.B., Skaar, T.C., Hamburger, D.S., Riggins, R.B., Fernandez, D.R., Zwart, A., Wang, A. & Clarke, R. “Tumor suppressor activities of interferon regulatory factor-1 in human breast cancer associated with caspase activation and induction of apoptosis.”, Carcinogenesis 26: 1527-1535, 2005. PubMed
  4. Clarke, R., Leonessa, F. & Trock, B. “Multidrug resistance/P-glycoprotein and breast cancer: review and meta-analysis.”, Semin Oncol, 32 (suppl 7): 9-15, 2005. PubMed
  5. Hilakivi-Clarke, L.A., Olivo, S.E., Shajahan, A., Khan, G., Zhu, Y., Zwart, A., Cho, E. & Clarke, R. “Mechanisms mediating the effects of prepubertal (n-3) polyunsaturated fatty acid diets on breast cancer risk in rats.”, J Nutr, 135 (suppl 12): 2946-2952, 2005. PubMed
  6. Ressom, H., Xuan, J., Wang, Y. & Clarke, R. “Classification of microarray data using machine learning methods.”, Trans Integrated Biomed Informatics Enabling Tech, 2: , 2005.

Year 2004
  1. Espinoza, L.A., Li, P., Lee, R., Wang, Y., Clarke, R. & Smulson, M.E. “Evaluation of gene expression profiles of keratinocytes in response to JP-8 jet fuel.”, Toxicol Appl Pharmacol, 200:93-102, 2004. PubMed
  2. Zhang, J., Wang, Y., Khan, J. & Clarke, R. “Gene selection in class space for molecular classification of cancer.”, Science in China Series F-Information Sciences 47: 301-314, 2004. SpringerLink
  3. Han, F., Miksicek, R., Clarke, R. & Conrad, S.E. “Expression of an estrogen receptor variant lacking exon 3 in derivatives of MCF-7 cells with acquired estrogen independence or Tamoxifen resistance.”, J Mol Endocrinol 32: 935-945, 2004.PubMed
  4. Bouker, K.B., Skaar, T.C., Fernandez, D.R., O’Brien, K.A., Riggins, R.B., Honghua, C. & Clarke, R. “Interferon regulatory factor-1 mediates the proapoptotic but not cell cycle arrest effects of the steroidal antiestrogen ICI 182,780 (Faslodex, Fulvestrant).”, Cancer Res, 64:4030-4039, 2004. PubMed
  5. Xuan, J., Dong, Y., Khan, J., Hoffman, E., Clarke, R. & Wang, Y. “Robust feature selection by weighted Fisher criterion for multiclass prediction in gene expression profiling.”, Proc Intl Conf Pattern Recon (17th International Conference) 2: 291-294, 2004. IEEE
  6. Thompson, E.W., Waltham, M., Ramus, S.J., Hutchins, A.-M., Armes, J.E., Campbell, I.G., Williams, E.D., Thompson, P.R., Rae, J.M., Johnson, M.D. & Clarke, R. “LCC15-MB cells are MDA-MB-435: A review of misidentified breast and prostate cell lines.”, Clin Exp Metastasis 21: 535-541, 2004. PubMed
  7. Wang, Y., Wang, Z., Xuan, J., Zhang, J., Hoffman, E.P., Clarke, R. & Khan, J. “Optimizing multilayer perceptrons by discriminatory component analysis.”, Proc IEEE Workshops Machine Learn Signal Process, Sao Luis, Brazil, pp. 273-282, 2004. IEEE
  8. Rae, J.M., Ramus, S.J., Waltham, M., Armes, J.E., Campbell, I.G., Clarke, R., Brandt, R., Johnson, M.D. & Thompson, E.W. “Common origins of MDA-MB-435 cells from various sources with those shown to have melanoma properties.”, Clin Exp Metastasis 21: 543-552, 2004. PubMed

Year 2003
  1. Leonessa, F. & Clarke, R. “ATP binding cassette transporters and drug resistance in breast cancer .”, Endocr Related Cancer, 10: 43-73, 2003. Endocr Related Cancer
  2. Wang, Y., Zhang, Z., Xuan, J., Khan, J. & Clarke, R. “Partially-independent component analysis for tissue heterogeneity correction in gene expression analysis.”, Proc IEEE Neural Netw Signal Processing, 279-288, 2003. IEEE
  3. Wang, Z., Wang, Y., Lu, J., Kung, S.-Y., Zhang, J., Lee, R., Xuan, J., Khan, J. & Clarke, R. “Discriminatory mining of gene expression microarray data.”, J VLSI Signal Process Sys 35: 255-272, 2003. ACM
  4. Clarke, R., Liu, M.C., Bouker, K.B., Gu, Z., Lee, R.Y., Zhu, Y., Skaar, T.C., Gomez, B., O'Brien, K., Wang, Y. & Hilakivi-Clarke, L.A. “Antiestrogen resistance in breast cancer and the role of estrogen receptor signaling.”, Oncogene 22: 7316-7339, 2003. PubMed
  5. Pratt, M.A.C., Bishop, T.E., White, D., Yasvinski, G., Ménard, M., Niu, M.Y. & Clarke, R. “Estrogen withdrawal-induced NF-κB and Bcl-3 expression in breast cancer cells: roles in growth and hormone independence.”, Mol Cell Biol 23: 6887-6900, 2003. PubMed
  6. Johnson, M., Kenney, N., Hilakivi-Clarke, L., Singh, S., Chepko, G., Newbold, R., Clarke, R., Sholler, P.F., Lirio, A.A., Foss, C., Trock, B., Paik, S., Stoica, A. & Martin, M.B. “Cadmium mimics the effects of estrogen in vivo in the uterus and mammary gland.”, Nature Med 9: 1081-1084, 2003. PubMed

Year 2002
  1. Hilakivi-Clarke, L.A., Cabanes, A., Olivo, S., Kerr, L., Bouker, K.B. & Clarke, R. “Do estrogens always increase breast cancer risk?”, J Steroid Biochem Mol Biol 80: 163-174, 2002. PubMed
  2. Poola, I., Clarke, R., Dewitty, R. & Lafalle, L.D. “Functionally active estrogen receptor isoforms in the breast tumors of African American women are different from the profiles in breast tumors of Caucasian women.”, Cancer 94: 615-623, 2002. PubMed
  3. Leonessa, F., Kim, J.-H., Ghiorghis, A., Kulawiec, R., Hammer, C., Talebian, A. & Clarke, R. “C-7 Analogs of progesterone as potent inhibitors of the P-Glycoprotein efflux pump.”, J Med Chem 45: 390-398, 2002. PubMed
  4. Wang, Y., Lu, J., Lee, R. & Clarke, R. “Iterative normalization of cDNA microarray data.”, IEEE Trans Inf Techol Biomed 6: 29-37, 2002. PubMed
  5. Clarke, R. & Dickson, R.B. “Animal models of endocrine responsive and unresponsive breast cancers.”, In: “Endocrine Management of Breast Cancer”, Eds: Robertson, J.F.R., Nicholson, R.I. & Hayes, D.F., Martin Dunitz, Ltd, London, U.K., 191-208, 2002.
  6. Gu, Z., Lee, Y.R., Skaar, T.C., Bouker, K.B., Welch, J.N., Lu, J., Liu, A., Davis, N., Wang, Y. & Clarke, R. “Association of interferon regulatory factor-1, nucleophosmin, nuclear factor-κB and cAMP response element binding with acquired resistance to Faslodex (ICI 182,780).”, Cancer Res 62: 1155-1166, 2002. Cancer Res
  7. Liu, A., Zhang, Y., Gehan, E. & Clarke, R. “Block principal components analysis with application to gene microarray data classification.”, Stat Med 21: 3465-3474, 2002. PubMed
  8. Ellis, M., Davis, N., Coop, A., Liu, M., Schumaker, L., Lee, R.Y., Srikanchana, R., Russell, C., Singh, B., Miller, W.R., Stearns, V., Pennanen, M., Tsangaris, T., Gallagher, A., Liu, A., Zwart, A., Hayes, D.F., Lippman, M.E., Wang, Y. & Clarke, R. “Development and validation of a method for using breast core needle biopsies for gene expression microarray analyses.”, Clin Cancer Res 8: 1155-1166, 2002. PubMed
  9. Welch, J.N. & Clarke, R. “ErbB-2 expression and drug resistance in cancer.”, Signal, 3: 4-9, 2002.
  10. Hilakivi-Clarke, L.A., Cho, E., Cabanes, A., DeAssis, S., Olivo, S., Helferich, W., Lippman, M.E. & Clarke, R. “Modulation of pregnancy estrogen levels by maternal dietary exposure to genistein or n-3 polyunsaturated fatty acids and breast cancer risk among female offspring.”, Clin Cancer Res 8: 3601-3610, 2002.
  11. Clarke, R. “Human breast cancer xenografts as models of the human disease.”, In: “Tumor Models in Cancer Research”, Ed: Teicher, B.A., Humana Press, Inc., New Jersey, pp 453-470, 2002.

Year 2001
  1. Lu, L., Leonessa, F., Clarke, R. & Wainer, I.W. “Competitive and allosteric interactions in ligand binding to P-glycoprotein as observed on an immobilized P-glycoprotein liquid chromatographic stationary phase.”, Mol Pharmacol 59: 62-68, 2001. PubMed
  2. Clarke, R. “Novel Molecular Targets and Drugs.”, IDrugs, 4: 504-506, 2001. BioMed
  3. Clarke, R. “Human tumors in animal hosts.”, In: “Cancer Handbook”, Nature Publishing Group Reference Ltd., London, U.K., pp 913-922, 2001.
  4. Clarke, R., Hilakivi-Clarke, L.A. & Trock, B. “Breast cancer: dietary and environmental oestrogens.”, Biologist, 48: 21-26, 2001. Biologist
  5. James, M.R., Skaar, T.C., Lee, R.Y., MacPherson, A., Zwiebel, J.A., Ahluwalia, B.S., Ampy, F. & Clarke, R. “Constitutive expression of the steroid sulfatase gene in estrogen-dependent MCF-7 human breast cancer cells.”, Endocrinology 142: 1497-1505, 2001. PubMed
  6. Clarke, R., Leonessa, F., Welch, J.N. & Skaar, T.C. “Cellular and molecular pharmacology of antiestrogen action and resistance.”, Pharmacol Rev 53: 25-72, 2001.PubMed
  7. Clarke, R., Skaar, T.C., Bouker, K.B., Davis, N., Lee, Y.R., Welch, J.N. & Leonessa, F. “Molecular and pharmacological aspects of antiestrogen resistance.”, J Steroid Biochem Mol Biol 76: 71-84, 2001. PubMed
  8. Lu, L., Leonessa, F., Baynham, M.T., Clarke, R., Gimenez, F., Pham, Y.-T., Roux, F. & Wainer, I.W. “The enantioselective binding of mefloquine enantiomers to P-glycoprotein determined using an immobilized P-glycoprotein liquid chromatographic stationary phase.”, Pharmaceut Res 18: 1327-1330, 2001. PubMed
  9. Hilakivi-Clarke, L.A., Cho, E., Assis, S., Olivo, S., Ealley, E., Bouker, K.B., Welch, J.N., Khan, G., Clarke, R. & Cabanes, A. “Maternal and prepubertal diet, mammary development and breast cancer risk.”, J Nutr 131: 154-157, 2001. PubMed
  10. Lu, J., Wang, Y., Xuan, J., Kung, S.Y., Gu, Z. & Clarke, R. “Discriminative mining of gene microarray data.”, Proc IEEE Neural Net Signal Process 11: 218-227, 2001. IEEE

Year 2000
  1. Zhang, Y., Leonessa, F., Clarke, R. & Wainer, I.W. “Development of an immobilization of P-glycoprotein stationary phase for on-line liquid chromatographic determination of drug binding affinities.”, J Chromatogr B 739: 33-37, 2000. J Chromatogr B
  2. Poola, I., Chatra, S., Koduri, S. & Clarke, R. “Identification of twenty alternatively spliced estrogen receptor alpha mRNAs in breast cancer cell lines and tumors using splice targeted primer approach.”, J Steroid Biochem Mol Biol 72: 249-258, 2000. PubMed
  3. Hilakivi-Clarke, L.A., Cho, E., Onojafe, I. & Clarke, R. “Maternal exposure to tamoxifen during pregnancy increases mammary tumorigenesis among female offspring.”, Clin Cancer Res 6: 305-308, 2000. PubMed
  4. Clarke, R. & Johnson, M.D. “Chapter 22: Animal models.”, In: “Diseases of the Breast” 2nd Edition. Eds: Harris, J.R., Lippman, M.E., Morrow, M., Hellman, S. Publisher: J. B. Lippincott Co., Philadelphia, pp 319-333, 2000.
  5. Clarke, R. “Sex steroids in the mammary gland.”, J Mammary Gland Biol Neoplasia 5: 245-250, 2000. PubMed
  6. Clarke, R. “Meeting report: 10th Annual American Institute for Cancer Research Conference - The Role of Nutrition in Preventing and treating Breast and Prostate Cancer.”, CD Current Drugs: ID Weekly Highlights, Sept., 21-24, 2000. PubMed
  7. Clarke, R., Leonessa, F., Brünner, N. & Thompson, E.W. “Chapter 23: In vitro models.”, In: “Diseases of the Breast” 2nd Edition. Eds: Harris, J.R., Lippman, M.E., Morrow, M., Hellman, S. Publisher: J. B. Lippincott Co., Philadelphia, pp 335-354, 2000.

Year 1999
  1. Hilakivi-Clarke, L.A., Trock, B. & Clarke, R. “The estrogenicity of selected nutrients, phytochemicals, pesticides and pollutants: their potential roles in breast cancer.”, In: “Breast Cancer, Molecular Genetics, Pathogenesis and Therapeutics. Series: Contemporary Cancer Research.” Ed: Bowcock, A. Publisher: Humana Press, Clifton, pp 537-568, 1999.
  2. Gopalakrishna, R., Gundimeda, U., Fontana, J.A. & Clarke, R. “Differential distribution and nuclear association of protein phosphatase 2A in human breast carcinoma cell lines and its relation to estrogen receptor status and tumor progression.”, Cancer Lett 136: 119-128, 1999. Cancer Lett
  3. Hilakivi-Clarke, L.A., Cho, E., Onojafe, I., Raygada, M. & Clarke, R. “Maternal exposure to genistein during pregnancy increases mammary tumorigenesis in female rat offspring.”, Oncol Rep 6: 1089-1095, 1999. PubMed
  4. Lavigne, M.C., Ramwell, P.W. & Clarke, R. “Growth regulation and ultrastructural characterization of porcine coronary artery smooth muscle cells.”, In Vitro Cell Dev Biol 35: 136-143, 1999.
  5. Plouzek, C.A., Morris, D.W., Clarke, R. & Yeh, G.C. “Rosemary: a new P-glycoprotein reversal agent of chemotherapeutic drugs in drug-resistant human breast cancer cells.”, Eur J Cancer 35: 1541-1545, 1999. PubMed
  6. Clarke, R., Skaar, T., El-Ashry, D., Leonessa, F. & Hilakivi-Clarke, L.A. “Use of ERE and reporter gene constructs to assess putative estrogenic activity.”, J Med Food 2: 127-133, 1999. PubMed
  7. Arteaga, C.L., Koli, K.M., Dugger, T.C. & Clarke, R. “Reversal of tamoxifen resistance of human breast carcinomas in vivo with neutralizing anti-transforming growth factor (TGF)-β antibodies.”, J Natl Cancer Inst, 91: 46-53, 1999. PubMed
  8. Lavigne, M.C., Ramwell, P.W. & Clarke, R. “The effects of estrogens and antiestrogens on the growth of porcine coronary artery smooth muscle cells.”, Steroids 64: 472-480, 1999. PubMed
  9. Hilakivi-Clarke, L.A., Onojafe, I., Raygada, M., Cho, E., Skaar, T. & Clarke, R. “Prepubertal exposure to zearalenone or genistein reduces mammary tumorigenesis.”, Br J Cancer 80: 1682-1688, 1999. PubMed
  10. Hilakivi-Clarke, L.A., Clarke, R. & Lippman, M.E. “The influence of maternal diet on breast cancer risk among female offspring”, Nutrition 15: 392-401, 1999. PubMed
  11. Thompson, E.W., Sung, V., Lavigne, M., Baumann, K., Azumi, N., Aaron, A.D. & Clarke, R. “LCC15-MB: a vimentin-positive human breast cancer cell line from a femoral bone metastasis.”, Clin Exptl Metastasis, 17: 193-204, 1999. SpringerLink

Year 1998
  1. Sung, V., Gilles, C., Murray, A., Clarke, R., Aaron, A.D., Azumi, N. & Thompson, E.W. “The LCC15-MB human breast cancer cell line expresses osteopontin and exhibits an invasive and metastatic phenotype”, Exptl Cell Res 241: 273-284, 1998. PubMed
  2. Brankin, B., Skaar, T.C., Trock, B., Berris, M. & Clarke, R. “Autoantibodies to the nucleolar phosphoprotein nucleophosmin in breast cancer patients”, Cancer Epidemiol Biomark Prev 7: 1109-1115, 1998. PubMed
  3. Skaar, T.C., Prasad, S.C., Sharareh, S., Brünner, N., Lippman, M.E. & Clarke, R. “Two-dimensional gel electrophoresis analyses identify nucleophosmin as an estrogen regulated protein associated with acquired estrogen-independence in human breast cancer cells.”, J Steroid Biochem Mol Biol 67: 391-402, 1998. PubMed
  4. Hilakivi-Clarke, L.A., Cho, E. & Clarke, R. “Maternal genistein exposure mimics the effects of estrogen on mammary gland development in female mouse offspring”, Oncol Rep 5: 609-616, 1998. PubMed
  5. Clarke, R. “Antiestrogen resistance”, Breast Cancer On-Line, http://www.bco.org, 1998.
  6. Hilakivi-Clarke, L.A. & Clarke, R. “Timing of dietary fat exposure and mammary tumorigenesis: role of estrogen receptor and protein kinase C activity”, Mol Cell Biochem, 188: 5-12, 1998. PubMed

Year 1997
  1. Brünner, N., Boysen, B., Jirus, S., Skaar, T.C., Holst-Hansen, C., Lippman, J., Frandsen, T., Spang-Thomsen, M., Fuqua, S.A.W. & Clarke, R. “MCF7/LCC9: an antiestrogen resistant MCF-7 variant where acquired resistance to the steroidal antiestrogen ICI 182,780 confers an early crossresistance to the non-steroidal antiestrogen tamoxifen.”, Cancer Res 57: 3486-3493, 1997. PubMed
  2. Hilakivi-Clarke, L.A., Clarke, R., Onojafe, I., Raygada, M., Cho, E. & Lippman, M.E. “A high-fat diet during pregnancy increases mammary epithelial density and breast cancer risk among female rat offspring.”, Proc Natl Acad Sci USA 94: 9372-9377, 1997. PubMed
  3. Trock, B., Leonessa, F. & Clarke, R. “Multidrug resistance in breast cancer: a meta-analysis of MDR1/gp170 expression and its possible functional significance.”, J Natl Cancer Inst 89: 917-931, 1997. PubMed
  4. Clarke, R. & Dickson, R.B. “Animal models of tumor onset, growth and metastasis.”, In: “Encyclopedia of Cancer: Volume I” Ed: Bertino, J.R. Publisher: Academic Press, San Diego, pp 10-21, 1997.
  5. Clarke, R. “Issues in experimental design and endpoint analysis in the study of experimental cytotoxic agents in vivo in breast cancer and other models.”, Breast Cancer Res Treat 46: 255-278, 1997. PubMed
  6. Clarke, R. “Animal models of breast cancer: experimental design and their use in nutrition and psychosocial research.”, Breast Cancer Res Treat 46: 117-133, 1997. PubMed
  7. Clarke, R., Leonessa, F. & Trock, B. “The role of MDR1/gp170 in human breast cancer (a meta analysis of published studies).”, In: “Era of Hope: The Department of Defense Breast Cancer Research Program. Volume III” pp 865-866, 1997.
  8. Jørgensen, L., Brünner, N., Spang-Thomsen, M., Clarke, R., Dombernowsky, P. & Svenstrup, B. “A comparative study of steroid metabolism in the hormone dependent MCF-7 human breast carcinoma cell line and its two hormone resistant subpopulations MCF7/LCC1 and MCF7/LCC2.”, J Steroid Biochem Mol Biol 63: 275-281, 1997. PubMed

Year 1996
  1. Clarke, R. & Brünner, N. “Acquired estrogen independence and antiestrogen resistance in breast cancer: estrogen receptor driven phenotypes?”, Trends Endocrinol Metab 7: 25-35, 1996. PubMed
  2. Clarke, R. & Lippman, M.E. “Mechanisms of resistance to antiestrogens and their implications for crossresistance.”, In: “Tamoxifen: Beyond the Antiestrogen.” Ed: Kellen, J.A. Publisher: Birkhäuser, Boston, pp 231-266, 1996.
  3. Clarke, R., Skaar, T., Leonessa, F., Brankin, B., James, M., Brünner, N. & Lippman, M.E. “The acquisition of an antiestrogen resistant phenotype in breast cancer: the role of cellular and molecular mechanisms.”, Cancer Treat Res 87: 263-283, 1996. PubMed
  4. Clarke, R., Hilakivi-Clarke, L.A., Cho, E., James, M.R. & Leonessa, F. “Estrogens, phytoestrogens and breast cancer.”, Adv Exp Med Biol 401: 63-85, 1996. PubMed
  5. Clarke, R. “Animal models of breast cancer: their diversity and role in biomedical research.”, Breast Cancer Res Treat 39: 1-6, 1996. PubMed
  6. Clarke, R. “Animal models of breast cancer.”, In: “Diseases of the Breast.” Eds: Harris, J.R., Lippman, M.E., Morrow, M., Hellman, S. Publisher: J. B. Lippincott Co., Philadelphia, pp 235-244, 1996.
  7. Hilakivi-Clarke, L.A., Raygada, M., Cho, E., Clarke, R. & Lippman, M. “Breast cancer risk in rats fed a diet high in n-6 polyunsaturated fatty acids during pregnancy.”, J Natl Cancer Inst 88: 121-127, 1996. PubMed
  8. Leonessa, F., Green, D., Licht, T., Wright, A., Wingate-Legette, K., Lippman, J., Gottesman, M.M. & Clarke, R. “MDA435/LCC6 and MDA435/LCC6MDR1: ascites models of human breast cancer.”, Br J Cancer 73:154-161, 1996. PubMed
  9. Bei, M., Lavigne, M.C., Foegh, M.L., Ramwell, P. & Clarke, R. “Specific binding of oestradiol to rat coronary artery heart smooth muscle cells.”, J Steroid Biochem Mol Biol 58: 83-88, 1996. PubMed
  10. Clarke, R. “Human breast cancer cell line xenografts as models of breast cancer - The immunobiologies of recipient mice and the characteristics of several tumorigenic cell lines.”, Breast Cancer Res Treat 39: 69-86, 1996. PubMed
  11. Clarke, R., Leonessa, F., Brünner, N. & Thompson, E.W. “In vitro models of breast cancer.”, In: “Diseases of the Breast.” Eds: Harris, J.R., Lippman, M.E., Morrow, M., Hellman, S. Publisher: J. B. Lippincott Co., Philadelphia, pp 245-261, 1996.

Year 1995
  1. Clarke, R. & Brünner, N. “Cross–resistance and molecular mechanisms in antiestrogen resistance.”, Endocr Related Cancer 2: 59-72, 1995. Endocr Related Cancer
  2. Ruiz-Cabello, J., Berghmans, K., Kaplan, O., Lippman, M.E., Clarke, R. & Cohen, J.S. “Hormone dependence of breast cancer cells and the effects of tamoxifen and estrogen: 31P NMR studies.”, Breast Cancer Res Treat 33: 209-217, 1995. PubMed
  3. Dickson, R.B. & Clarke, R. “Breast Cancer: new biological approaches to treatment.”, In: “Molecular Endocrinology of Cancer.” Ed: Waxman, J. Publisher: Cambridge University Press, Cambridge, UK: pp 271-303, 1995.
  4. Hilakivi-Clarke, L.A., Cho, E., Raygada, M., Clarke, R. & Lippman, M.E. “Early life affects the risk to develop breast cancer.”, Ann NY Acad Sci 768: 327-330, 1995. PubMed
  5. Brünner, N., Johnson, M.D., Holst-Hansen, J.F., Kiilgaard, J.F., Thompson, E.W. & Clarke, R. “Acquisition of estrogen independence and antiestrogen resistance in breast cancer: association with the invasive and metastatic phenotype.”, Endocr Related Cancer 2: 27-36, 1995. Endocr Related Cancer
  6. Kristensen, C.A., Kristjansen, P.E.G., Brünner, N., Clarke, R., Spang-Thomsen, M. & Quistorff, B. “Effect of estrogen withdrawal and prediction of estrogen dependence monitored by in vivo 31P magnetic resonance spectroscopy of four human breast cancer xenografts.”, Cancer Res 55: 1664-1669, 1995. PubMed

Year 1994
  1. Zyad, A., Bernard, J., Clarke, R., Tursz, T., Brockhaus, M. & Chouaib, S. “Human breast cancer cross-resistance to TNF and adriamycin: relationship to MDR1, MnSOD and TNF gene expression.”, Cancer Res 54: 825-831, 1994. PubMed
  2. Leonessa, F., Jacobson, M., Boyle, B., Lippman, J., McGarvey, M. & Clarke, R. “The effect of tamoxifen on the multidrug resistant phenotype in human breast cancer cells: isobologram, drug accumulation, and gp-170 binding studies.”, Cancer Res 54: 441-447, 1994. PubMed
  3. Clarke, R. & Leonessa, F. “Cytotoxic drugs and hormones in breast cancer: interactions at the cellular level.”, In: “Drug and Hormonal Resistance in Breast Cancer” Eds: Lippman, M.E. and Dickson, R.B. Publisher: Ellis Horwood, Inc. New York, pp 407-432, 1994.
  4. Hilakivi-Clarke, L.A., Clarke, R. & Lippman, M.E. “Perinatal factors increase breast cancer risk.”, Breast Cancer Res Treat 31: 273-284, 1994. PubMed
  5. Coopman, P., Garcia, M., Brünner, N., Derocq, D., Clarke, R. & Rochefort, H. “Antiproliferative and antiestrogenic effects of ICI 164,384 in 4-OH-Tamoxifen-resistant human breast cancer cells.”, Int J Cancer 56: 295-300, 1994. PubMed
  6. Clarke, R., Skaar, T., Baumann, K., Leonessa, F., James, M.R., Lippman, J., Thompson, E.W., Freter, C. & Brünner, N. “Hormonal carcinogenesis in breast cancer: cellular and molecular studies of malignant progression.”, Breast Cancer Res Treat 31: 237-248, 1994. PubMed

Year 1993
  1. Hilakivi-Clarke, L.A., Rowland, J., Clarke, R. & Lippman, M.E. “Psychosocial factors in the development and progression of breast cancer.”, Breast Cancer Res Treat 29: 141-160, 1993. PubMed
  2. Brünner, N., Boulay, V., Fojo, A., Freter, C., Lippman, M.E. & Clarke, R. “Acquisition of hormone-independence in MCF-7 cells is accompanied by increased expression of estrogen regulated genes but without DNA amplifications.”, Cancer Res 53: 283-290, 1993. PubMed
  3. Brünner, N., Frandsen, T.O., Holst-Hansen, C., Bei, M., Thompson, E.W., Wakeling, A.E., Lippman, M.E. & Clarke, R. “MCF7/LCC2: A 4-hydroxytamoxifen resistant human breast cancer variant which retains sensitivity to the steroidal antiestrogen ICI 182,780.”, Cancer Res 53: 3229-3232, 1993. PubMed
  4. Hilakivi-Clarke, L.A., Arora, P.K., Clarke, R., Wright, A. & Dickson, R.B. “Opposite behavioral alterations in male and female transgenic TGFα mice: association with tumorigenesis.”, Br J Cancer 67: 1026-1030, 1993. PubMed
  5. Clarke, R., Thompson, E.W., Leonessa, F., Lippman, J., McGarvey, M. & Brünner, N. “Hormone resistance, invasiveness and metastatic potential in human breast cancer.”, Breast Cancer Res Treat 24: 227-239, 1993. PubMed
  6. Clarke, R. & Lippman, M.E. “The acquisition of antiestrogen resistance in breast cancer”, In: “Drug Resistance in Oncology.” Eds: Teicher, B.A. Publisher: Marcel Dekker, Inc., New York, pp 501-536, 1993.
  7. Thompson, E.W., Brünner, N., Torri, J., Boulay, V., Wright, A., Lippman, M.E., Steeg, P.S. & Clarke, R. “The invasive and metastatic properties of hormone-independent but hormone-responsive variants of MCF-7 human breast cancer cells.”, Clin Exptl Metastasis 11: 15-26, 1993. PubMed

Year 1992
  1. Hilakivi-Clarke, L.A., Arora, P., Sabol, M.-B., Clarke, R., Dickson, R.B. & Lippman, M.E. “Alterations in behavior, steroid hormones and natural killer cell activity in male transgenic TGFα-mice.”, Brain Res 588: 97-103, 1992. PubMed
  2. Ghiorghis, A., Talebian, A. & Clarke, R. “In vitro antineoplastic activity of N7-substituted mitomycin C analogues against human breast cancer cell lines.”, Cancer Chemother Pharmacol 29: 290-296, 1992. PubMed
  3. Clarke, R., Lippman, M.E. & Dickson, R.B. “Hormonal aspects of breast cancer: growth factors, drugs and stromal interactions.”, Crit Rev Oncol Hematol 12: 1-23, 1992. PubMed
  4. Leonessa, F., Boulay, V., Wright, A., Thompson, E.W., Brünner, N. & Clarke, R. “The biology of breast tumor progression: acquisition of hormone-independence and resistance to cytotoxic drugs.”, Acta Oncol 31: 115-123, 1992. PubMed
  5. Farhat, M., Abi-Younes, S., Vargas, R., Wolfe, R.M., Clarke, R. & Ramwell, P.W. “Vascular non-genomic effects of estrogen.”, In: “Sex Steroids and the Cardiovascular System”. Eds: Ramwell, P.W., Rubanyi, G. & Schillinger, E. Publisher: Springer-Verlag, Berlin, pp 145-159, 1992.
  6. Thompson, E.W., Paik, S., Brünner, N., Sommers, C.L., Clarke, R., Zugmaier, G., Shima, T.B., Torri, J., Donahue, S., Lippman, M.E. & Dickson, R.B. “Association of increased basement membrane-invasiveness with the absence of estrogen receptor and expression of vimentin in human breast cancer cell lines.”, J Cell Physiol 150: 534-544, 1992. PubMed
  7. Brünner, N., Moser, C., Clarke, R. & Cullen, K. “IGF-I and IGF-II expression in human breast cancer xenografts: relationship to hormone-independence.”, Breast Cancer Res Treat 22: 39-45, 1992. PubMed
  8. Clarke, R., Currier, S., Kaplan, O., Boulay, V., Gottesman, M. & Dickson, R.B. “Effect of P-glycoprotein expression on sensitivity to hormones in MCF-7 human breast cancer cells.”, J Natl Cancer Inst 84: 1506-1512, 1992. PubMed
  9. Lehtola, L., Partanen, J., Sistonen, L., Korhonen, J., Warri, A., Clarke, R. & Alitalo, K. “Analysis of tyrosine kinase mRNAs including three FGF receptor-like genes from the MCF-7 breast carcinoma cells.”, Int J Cancer 50: 598-603, 1992. PubMed
  10. Yano, T., Pinski, J., Szepeshazi, K., Korkut, E., Groot, K., Clarke, R., Comaru-Schally, A.M. & Schally, A.V. “Growth inhibition of human breast carcinoma (MCF-7 MIII) in athymic nude mice with sustained delivery systems of luteinizing hormone-releasing hormone antagonist SB-75 and agonist D-Trp6-LH-RH.”, Breast Cancer Res Treat 21: 35-45, 1992. PubMed

Year 1991
  1. Kaplan, O., Jaroszewski, J.W., Clarke, R., Fairchild, C.R., Schoenlein, P., Goldenberg, S., Gottesman, M.M. & Cohen, J. “The multi-drug resistance phenotype: 31P NMR characterization and 2-deoxyglucose toxicity.”, Cancer Res 51: 1638-1644, 1991. PubMed
  2. Clarke, R., Dickson, R.B. & Lippman, M.E. “The role of steroid hormones and growth factors in the control of normal and malignant breast.”, In: “Structure and Function of Nuclear Hormone Receptors” Ed: Parker, M.G. Publisher: Academic Press Ltd., pp297-319, 1991.
  3. Clarke, R. & Dickson, R.B. “The interactions among steroid hormones, steroid hormone receptors, antiestrogens, biological response modifiers and cytotoxic drugs in human breast cancer.”, BMS Cancer Symposia 13: 223-253, 1991.

Year 1990
  1. Clarke, R., Dickson, R.B. & Brünner, N. “The process of malignant progression in human breast cancer.”, Ann Oncol 1: 401-407, 1990. PubMed
  2. Clarke, R., Lippman, M.E. & Dickson, R.B. “Mechanism of hormone and cytotoxic drug interactions in the development and treatment of breast cancer.”, Prog Clin Biol Res 322: 243-278, 1990. PubMed
  3. Clarke, R., van den Berg, H.W. & Murphy, R.F. “Tamoxifen and 17β-estradiol reduce the membrane fluidity of human breast cancer cells.”, J Natl Cancer Inst 82: 1702-1705, 1990. PubMed
  4. Brünner, N., Clarke, R., Lippman, M.E. & Dickson, R.B. “Models for studying the progression from hormone-dependence to independency in human breast cancer.”, In: “Growth Regulation of Cancer II” Eds: Lippman, M.E. & Dickson, R.B. Publisher: Alan R. Liss Inc., pp 115-126, 1990.

Year 80s
  1. Clarke, R., Brünner, N., Thompson, E.W., Glanz, P., Katz, D., Dickson, R.B. & Lippman, M.E. “The inter-relationships between ovarian-independent growth, antioestrogen resistance and invasiveness in the malignant progression of human breast cancer.”, J Endocrinol 122: 331-340, 1989. PubMed
  2. Clarke, R., Brünner, N., Katz, D., Glanz, P., Dickson, R.B., Lippman, M.E. & Kern, F. “The effects of a constitutive production of TGF-alpha on the growth of MCF-7 human breast cancer cells in vitro and in vivo.”, Mol Endocrinol 3: 372-380, 1989. PubMed
  3. Clarke, R., Brünner, N., Katzenellenbogen, B.S., Thompson, E.W., Norman, M.J., Koppi, C., Paik, S., Lippman, M.E. & Dickson, R.B. “Progression from hormone dependent to hormone independent growth in MCF-7 human breast cancer cells.”, Proc Natl Acad Sci USA 86: 3649-3653, 1989. PubMed
  4. Clarke, R. & van den Berg, H.W. “Adverse interactions between cytotoxic drugs and hormonal agents in human breast cancer cells.”, J Clin Oncol 7: 1580-1582, 1989. PubMed
  5. Cullen, K.J., Yee, D., Bates, S.E., Brünner, N., Clarke, R., Dickson, R.B., Huff, K.K., Paik, S., Rosen, N., Valverius, E., Zugmaier, G. & Lippman, M.E. “Regulation of human breast cancer by secreted growth factors.”, Acta Oncol 28: 835-839, 1989. PubMed
  6. Brünner, N., Zugmaier, G., Bano, M., Ennis, B.W., Clarke, R., Cullen, K.J., Kern, F.G., Dickson, R.B. & Lippman, M.E. “Role of secreted polypeptides in growth regulation of breast cancer.”, Cancer Cells 1: 81-86, 1989.
  7. Brünner, N., Poulsen, H.S., Clarke, R. & Spang-Thomsen, M. “Effect of oophorectomy (Ovax) on estrogen receptor (ER) and progesterone receptor (PGR) concentration in an ovarian dependent and an ovarian independent ER and PGR positive human breast cancer grown in nude mice.”, In: “Immune-Deficient Animals in Experimental Medicine” Eds: Wu, B. & Zheng, J. Publisher: Karger, pp 196-201, 1989.
  8. Clarke, R., Lippman, M., Dickson, R.B. & Brünner, N. “In vivo\in vitro selection of hormone independent cells from the hormone dependent MCF-7 human breast cancer cell line.”, In: “Immune-Deficient Animals in Experimental Medicine” Eds: Wu, B. & Zheng, J. Publisher: Karger, pp 190-195, 1989.
  9. Thompson, E.W., Martin, M.B., Saceda, M., Clarke, R., Brünner, N., Lippman, M.E. & Dickson, R.B. “Regulation of breast cancer cells by hormones and growth factors: effects on proliferation and basement membrane invasiveness.”, Hormone Res 32 (suppl 1): 242-249, 1989. PubMed
  10. Dickson, R.B., Bates, S.E., Valverius, E., Knabbe, C., Salomon, D., Huff, K.K., Bronzert, D., Walker-Jones, D., Freter, C., Favoni, R., Yee, D., Zugmaier, G., Ennis, B., Clarke, R., Kern, F., Rosen, N. & Lippman, M.E. “Estrogen and antiestrogen regulation of mitogenic growth factors in human breast cancer cells.”, Prog Cancer Res Ther 35: 217-222, 1988.
  11. Han, K.-H., Niu, C.-H., Lokeshwar, V., Clarke, R., Katz, D. & Ferretti, J.A. “Conformational and receptor binding properties of human EGF and TGF-alpha second loop fragments.”, J Mol Recognition 1: 116-123, 1988. PubMed
  12. Cremin, M., Clarke, R., Nelson, J. & Murphy, R.F. “The response of human breast cancer cells to glucagon.”, Biochem Soc Trans 15: 241-242, 1987.
  13. van den Berg, H.W., Leahey, W.J., Lynch, M., Clarke, R. & Nelson, J. “Recombinant human interferon alpha increases oestrogen receptor expression in human breast cancer cells (ZR-75-1) and sensitises them to the anti-proliferative effects of Tamoxifen.”, Br J Cancer 55: 255-257, 1987. PubMed
  14. Nelson, J., Clarke, R. & Murphy, R.F. “The unoccupied estrogen receptor: some comments on localization.”, Steroids 48: 121-124, 1987. PubMed
  15. Clarke, R., van den Berg, H.W. & Murphy, R.F. “The ability of oestrogen to modulate the effects of cytotoxic drugs in human breast cancer cells; influence of oestrogen receptor (ER) status and choice of drug.”, Biochem Soc Trans 15: 242-243, 1987.
  16. Nelson, J., Clarke, R., McFerran, N.V. & Murphy, R.F. “Morpho-functional effects of phenol red on oestrogen sensitive human breast cancer cells.”, Biochem Soc Trans 15: 244-245, 1987.
  17. Cremin, M., Clarke, R., Nelson, J. & Murphy, R.F. “The response of human breast cancer cells to glucagon.”, Biochem Soc Trans 15: 241-242, 1987.
  18. Clarke, R., Morwood, J., van den Berg, H.W., Nelson, J. & Murphy, R.F. “Influence of vincristine on the oestrogen binding capacity of two human breast cancer cell lines in vitro.”, Biochem Soc Trans 14: 449-450, 1986.
  19. Kennedy, D.G., van den Berg, H.W., Clarke, R. & Murphy, R.F. “Enhancement of the sensitivity of MDA-MB-436 human breast cancer cell line to methotrexate by dipyridamole.”, Biochem Pharmacol 35: 3053-3056, 1986. PubMed
  20. Nelson, J., Clarke, R., Dickson, G.R., van den Berg, H.W. & Murphy, R.F. “The effects of Mg++ ions on nuclear integrity and apparent subcellular distribution of unoccupied oestrogen receptor in breast cancer cells.”, J Steroid Biochem 25: 619-626, 1986. PubMed
  21. Clarke, R., Morwood, J., van den Berg, H.W., Nelson, J. & Murphy, R.F. “The effect of cytotoxic drugs on estrogen receptor expression and response to Tamoxifen in MCF-7 cells.”, Cancer Res 46: 6116-6119, 1986. PubMed
  22. Nelson, J., Clarke, R., Dickson, G.R., van den Berg, H.W. & Murphy, R.F. “The effects of Mg++ or EDTA on the subcellular distribution of unoccupied estrogen receptor in ZR-75-1 and MCF-7 cells.”, Biochem Soc Trans 14: 447, 1986. PubMed
  23. Kennedy, D.G., van den Berg, H.W., Clarke, R. & Murphy, R.F. “The effect of the rate of cell proliferation on the synthesis of methotrexate poly-γ-glutamates in two human breast cancer cell lines.”, Biochem Pharmacol 34: 3087-3090, 1985. PubMed
  24. Kennedy, D.G., van den Berg, H.W., Clarke, R. & Murphy, R.F. “The effect of leucovorin on the synthesis of methotrexate poly-γ-glutamates in the MCF-7 human breast cancer cell line.”, Biochem Pharmacol 34: 2897-2903, 1985. PubMed
  25. Clarke, R., van den Berg, H.W., Kennedy, D.G. & Murphy, R.F. “Oestrogen receptor status and the response of human breast cancer cells to a combination of methotrexate and 17β-oestradiol.”, Br J Cancer 51: 365-369, 1985. PubMed
  26. Kennedy, D.G., Clarke, R., van den Berg, H.W. & Murphy, R.F. “The kinetics of methotrexate polyglutamate formation and efflux in a human breast cancer cell line (MDA-MB-436): the effect of insulin.”, Biochem Pharmacol 32: 41-46, 1983. PubMed
  27. Clarke, R., van den Berg, H.W., Kennedy, D.G. & Murphy, R.F. “Reduction of the antimetabolic and antiproliferative effects of methotrexate by 17β-oestradiol in a human breast carcinoma cell line (MDA-MB-436).”, Eur J Cancer Clin Oncol 19: 19-24, 1983. PubMed
  28. van den Berg, H.W., Clarke, R. & Murphy, R.F. “Failure of 5-fluorouracil and methotrexate to destroy the reproductive integrity of a human breast cancer cell line (MCF-7) growing in vitro.”, Eur J Cancer Clin Oncol 17: 1275-1281, 1981. PubMed